Bacterial endophytes inhabiting medicinal plants are less explored, but are diverse and play crucial roles in regulating growth and development of the host. Metagenomics using Illumina MiSeq platform facilitate whole community level characterization. The present study reports the diversity of bacterial endophytic microflora from the medicinal plant Emilia sonchifolia (Linn.)DC. Metagenomic analysis of medicinal plants leads to the identification of novel organisms or genes which will help the correlative elucidation of plant-microbe interactions. Effective sequences were amplified from 16S rRNA gene V3-V4 variable region. OTU analysis at different taxonomic level clearly catalogues two Phyla viz. Proteobacteria and Firmicutes which belonged to Gammaproteobacteria and Bacilli. In these classes five orders such as Enterobacteriales, Pseudomonadales, Xanthomonadales, Bacillales and Betaproteobacteriales were detected. Among these orders five families were identified in which the most predominant was Enterobacteriaceae and Pseudomonadeaceae while the other three families viz. Xanthomanadaceae, Planococcaceae and Burkholderiaceae were less represented. At genus level very less number of bacteria were identified while a bulk majority remained unclassified. Of the seven identified genus the most prominent one was Pseudomonas followed by Stenotrophomonas, Cronobacter, Lysinibacillus, Pantoea, Kluyvera and Pseudorhodoferax. At species level only two were identified vz. Pseudomonas otitidis and P.geniculate. Alpha diversity analysis using various statistical indices like Simpson and Shannon explains the diversity of microbiome. Next generation sequencing survey of DNA sample extracted from host plant through metagenomic data screening identified different endophytic bacteria which are difficult to grow in culture conditions.